Table 4.

Sequence uniqueness strongly impacts assembly coverage

	H3 assembly	A4 assembly control
Coding sequence (CDS)	94.0%	97.9%
Exon	93.9%	99.5%
Long noncoding RNA	90.6%	98.8%
microRNA	93.7%	99.6%
tRNA	76.5%	98.7%
Mobile genetic elements	55.3%	82.0%

The columns are H3 assembly without any polishing and a non-reference control assembly of standard coverage and size. The rows are annotation types. The value corresponds to the percent of aligned annotated elements with at least 90% of their sequence captured in our assembly. The coverage distribution of our assembly is bimodal, with the vast majority of elements being either covered by a single assembled contig or not covered at all. An expanded table including more annotation types and counts, polished versions of the assembly, and overall assembly statistics can be found in the supplement (Supplementary Table S1).